Evaluation of de novo transcriptome assemblies from RNA-Seq data
Li, Bo, Fillmore, Nathanael, Bai, Yongsheng, Collins, Mike, Thomson, James A, Stewart, Ron, Dewey, Colin N
Published in Genome biology (21.12.2014)
Published in Genome biology (21.12.2014)
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Journal Article
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Haas, Brian J, Papanicolaou, Alexie, Yassour, Moran, Grabherr, Manfred, Blood, Philip D, Bowden, Joshua, Couger, Matthew Brian, Eccles, David, Li, Bo, Lieber, Matthias, MacManes, Matthew D, Ott, Michael, Orvis, Joshua, Pochet, Nathalie, Strozzi, Francesco, Weeks, Nathan, Westerman, Rick, William, Thomas, Dewey, Colin N, Henschel, Robert, LeDuc, Richard D, Friedman, Nir, Regev, Aviv
Published in Nature protocols (01.08.2013)
Published in Nature protocols (01.08.2013)
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Journal Article
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive
Bernstein, Matthew N, Doan, AnHai, Dewey, Colin N
Published in Bioinformatics (Oxford, England) (15.09.2017)
Published in Bioinformatics (Oxford, England) (15.09.2017)
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Journal Article
RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis
Mehta, Charu, Fraga de Andrade, Isabela, Matson, Daniel R, Dewey, Colin N, Bresnick, Emery H
Published in Nucleic acids research (20.09.2021)
Published in Nucleic acids research (20.09.2021)
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Journal Article
Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema
Stewart, Ron, Rascón, Cynthia Alexander, Tian, Shulan, Nie, Jeff, Barry, Chris, Chu, Li-Fang, Ardalani, Hamisha, Wagner, Ryan J, Probasco, Mitchell D, Bolin, Jennifer M, Leng, Ning, Sengupta, Srikumar, Volkmer, Michael, Habermann, Bianca, Tanaka, Elly M, Thomson, James A, Dewey, Colin N
Published in PLoS computational biology (01.03.2013)
Published in PLoS computational biology (01.03.2013)
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Journal Article
CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology
Bernstein, Matthew N., Ma, Zhongjie, Gleicher, Michael, Dewey, Colin N.
Published in iScience (22.01.2021)
Published in iScience (22.01.2021)
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Journal Article
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans
Begun, David J, Holloway, Alisha K, Stevens, Kristian, Hillier, Ladeana W, Poh, Yu-Ping, Hahn, Matthew W, Nista, Phillip M, Jones, Corbin D, Kern, Andrew D, Dewey, Colin N, Pachter, Lior, Myers, Eugene, Langley, Charles H
Published in PLoS biology (01.11.2007)
Published in PLoS biology (01.11.2007)
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Journal Article
Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome
Hewitt, Kyle J., Kim, Duk Hyoung, Devadas, Prithvia, Prathibha, Rajalekshmi, Zuo, Chandler, Sanalkumar, Rajendran, Johnson, Kirby D., Kang, Yoon-A., Kim, Jin-Soo, Dewey, Colin N., Keles, Sunduz, Bresnick, Emery H.
Published in Molecular cell (02.07.2015)
Published in Molecular cell (02.07.2015)
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Journal Article
Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability
Jiang, Peng, Nelson, Jeffrey D., Leng, Ning, Collins, Michael, Swanson, Scott, Dewey, Colin N., Thomson, James A., Stewart, Ron
Published in Developmental biology (15.06.2017)
Published in Developmental biology (15.06.2017)
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Journal Article
Cell Type-Specific Transcriptome Profiling Reveals a Role for Thioredoxin During Tumor Initiation
Korte, Benjamin G, Giese, Morgan A, Ramakrishnan, Gayathri, Ma, Stella, Bennin, David, Rindy, Julie, Dewey, Colin N, Huttenlocher, Anna
Published in Frontiers in immunology (17.02.2022)
Published in Frontiers in immunology (17.02.2022)
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Journal Article
Infection induced inflammation impairs wound healing through IL-1β signaling
Shen, Simone, Miskolci, Veronika, Dewey, Colin N., Sauer, John-Demian, Huttenlocher, Anna
Published in iScience (19.04.2024)
Published in iScience (19.04.2024)
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Journal Article
Fine-scale phylogenetic discordance across the house mouse genome
White, Michael A, Ané, Cécile, Dewey, Colin N, Larget, Bret R, Payseur, Bret A
Published in PLoS genetics (01.11.2009)
Published in PLoS genetics (01.11.2009)
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Journal Article
Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping
Zeng, Xin, Li, Bo, Welch, Rene, Rojo, Constanza, Zheng, Ye, Dewey, Colin N, Keleş, Sündüz
Published in PLoS computational biology (01.10.2015)
Published in PLoS computational biology (01.10.2015)
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Journal Article
Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase
Sanchez-Vazquez, Patricia, Dewey, Colin N., Kitten, Nicole, Ross, Wilma, Gourse, Richard L.
Published in Proceedings of the National Academy of Sciences - PNAS (23.04.2019)
Published in Proceedings of the National Academy of Sciences - PNAS (23.04.2019)
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Journal Article
Distinctive populations of CD4+T cells associated with vaccine efficacy
Woodring, Therese, Dewey, Colin N., Santos Dias, Lucas Dos, He, Xin, Dobson, Hannah E., Wüthrich, Marcel, Klein, Bruce
Published in iScience (16.09.2022)
Published in iScience (16.09.2022)
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Journal Article
Bicaudal-C spatially controls translation of vertebrate maternal mRNAs
Zhang, Yan, Cooke, Amy, Park, Sookhee, Dewey, Colin N, Wickens, Marvin, Sheets, Michael D
Published in RNA (Cambridge) (01.11.2013)
Published in RNA (Cambridge) (01.11.2013)
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Journal Article
RNA-Seq gene expression estimation with read mapping uncertainty
Li, Bo, Ruotti, Victor, Stewart, Ron M., Thomson, James A., Dewey, Colin N.
Published in Bioinformatics (15.02.2010)
Published in Bioinformatics (15.02.2010)
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